Most Atari Lynx game boxes come in a relatively compact size to match the compact nature of the Lynx game cartridges. However, some of Atari's original releases (Chip's Challenge, Electrocop, Gates to Zendocon, etc.) were released in slightly larger boxes, and these boxes are more difficult to find nowadays. Atari's Lynx games came in two distinct visual styles. Earlier games feature a large Lynx logo at the top of the box, and a gray pattern adorned with the X from the Lynx logo along the right edge (this same pattern is used on the sides of all Atari's Lynx releases). Later releases contain a black border on the front of the box that encapsulates the game's name and artwork, with a smaller Lynx logo at the bottom. In addition, these later releases typically feature multiple languages on the back. There are other box styles, such as those produced by Williams/Shadowsoft and Telegames, although they don't deviate far from the style Atari used.

Games released in recent years have been shipped in plastic CD jewel cases, plastic baggies, orange plastic boxes, and other types of packaging. It's fairly easy to find Lynx games complete in the box, and many video game dealers have large stocks of brand new Lynx titles. In addition, Songbird Productions also sells new Lynx games and continues to develop new titles. If you're a collector who must have the box for every game in your collection, you'll find that the only thing holding you back from quickly realizing that goal on the Lynx will be your wallet.